generated: '2026-07-20' method: derived status: candidate source: openapi/one-codex-openapi-original.json server: name: one-codex transport: http url: null notes: No official hosted/remote One Codex MCP server was found. Candidate tool list derived one-per-operation from the OpenAPI 3.1 spec (170 operations). The official `onecodex` Python client is the supported programmatic surface. tools: - name: get_account_instances description: GET account instances source_operation: openapi/one-codex-openapi-original.json#get_account_instances - name: get_alignments_instances description: GET alignments instances source_operation: openapi/one-codex-openapi-original.json#get_alignments_instances - name: get_alignments_instances_public description: GET alignments instances_public source_operation: openapi/one-codex-openapi-original.json#get_alignments_instances_public - name: get_alignments_self description: GET alignments source_operation: openapi/one-codex-openapi-original.json#get_alignments_self - name: post_alignments_cancel description: POST alignments cancel source_operation: openapi/one-codex-openapi-original.json#post_alignments_cancel - name: get_alignments_file_details description: GET alignments file_details source_operation: openapi/one-codex-openapi-original.json#get_alignments_file_details - name: delete_alignments_files description: DELETE alignments files source_operation: openapi/one-codex-openapi-original.json#delete_alignments_files - name: get_alignments_files description: GET alignments files source_operation: openapi/one-codex-openapi-original.json#get_alignments_files - name: get_alignments_logs description: GET alignments logs source_operation: openapi/one-codex-openapi-original.json#get_alignments_logs - name: post_alignments_rerun description: POST alignments rerun source_operation: openapi/one-codex-openapi-original.json#post_alignments_rerun - name: get_alignments_results description: GET alignments results source_operation: openapi/one-codex-openapi-original.json#get_alignments_results - name: get_analyses_instances description: GET analyses instances source_operation: openapi/one-codex-openapi-original.json#get_analyses_instances - name: get_analyses_instances_public description: GET analyses instances_public source_operation: openapi/one-codex-openapi-original.json#get_analyses_instances_public - name: get_analyses_self description: GET analyses source_operation: openapi/one-codex-openapi-original.json#get_analyses_self - name: post_analyses_cancel description: POST analyses cancel source_operation: openapi/one-codex-openapi-original.json#post_analyses_cancel - name: get_analyses_file_details description: GET analyses file_details source_operation: openapi/one-codex-openapi-original.json#get_analyses_file_details - name: delete_analyses_files description: DELETE analyses files source_operation: openapi/one-codex-openapi-original.json#delete_analyses_files - name: get_analyses_files description: GET analyses files source_operation: openapi/one-codex-openapi-original.json#get_analyses_files - name: get_analyses_logs description: GET analyses logs source_operation: openapi/one-codex-openapi-original.json#get_analyses_logs - name: post_analyses_rerun description: POST analyses rerun source_operation: openapi/one-codex-openapi-original.json#post_analyses_rerun - name: get_analyses_results description: GET analyses results source_operation: openapi/one-codex-openapi-original.json#get_analyses_results - name: get_annotation_sets_instances description: GET annotation_sets instances source_operation: openapi/one-codex-openapi-original.json#get_annotation_sets_instances - name: get_annotation_sets_self description: GET annotation_sets source_operation: openapi/one-codex-openapi-original.json#get_annotation_sets_self - name: post_annotation_sets_download_csv description: POST annotation_sets download_csv source_operation: openapi/one-codex-openapi-original.json#post_annotation_sets_download_csv - name: post_annotation_sets_download_uri description: POST annotation_sets download_uri source_operation: openapi/one-codex-openapi-original.json#post_annotation_sets_download_uri - name: get_assemblies_instances description: GET assemblies instances source_operation: openapi/one-codex-openapi-original.json#get_assemblies_instances - name: get_assemblies_self description: GET assemblies source_operation: openapi/one-codex-openapi-original.json#get_assemblies_self - name: post_assemblies_download_uri description: POST assemblies download_uri source_operation: openapi/one-codex-openapi-original.json#post_assemblies_download_uri - name: get_assets_instances description: GET assets instances source_operation: openapi/one-codex-openapi-original.json#get_assets_instances - name: post_assets_instances_confirm_multipart_upload description: POST assets instances_confirm_multipart_upload source_operation: openapi/one-codex-openapi-original.json#post_assets_instances_confirm_multipart_upload - name: post_assets_instances_init_multipart_upload description: POST assets instances_init_multipart_upload source_operation: openapi/one-codex-openapi-original.json#post_assets_instances_init_multipart_upload - name: delete_assets_self description: DELETE assets source_operation: openapi/one-codex-openapi-original.json#delete_assets_self - name: get_assets_self description: GET assets source_operation: openapi/one-codex-openapi-original.json#get_assets_self - name: patch_assets_self description: PATCH assets source_operation: openapi/one-codex-openapi-original.json#patch_assets_self - name: post_assets_download_uri description: POST assets download_uri source_operation: openapi/one-codex-openapi-original.json#post_assets_download_uri - name: get_classifications_instances description: GET classifications instances source_operation: openapi/one-codex-openapi-original.json#get_classifications_instances - name: get_classifications_instances_public description: GET classifications instances_public source_operation: openapi/one-codex-openapi-original.json#get_classifications_instances_public - name: get_classifications_self description: GET classifications source_operation: openapi/one-codex-openapi-original.json#get_classifications_self - name: post_classifications_cancel description: POST classifications cancel source_operation: openapi/one-codex-openapi-original.json#post_classifications_cancel - name: get_classifications_file_details description: GET classifications file_details source_operation: openapi/one-codex-openapi-original.json#get_classifications_file_details - name: delete_classifications_files description: DELETE classifications files source_operation: openapi/one-codex-openapi-original.json#delete_classifications_files - name: get_classifications_files description: GET classifications files source_operation: openapi/one-codex-openapi-original.json#get_classifications_files - name: get_classifications_logs description: GET classifications logs source_operation: openapi/one-codex-openapi-original.json#get_classifications_logs - name: get_classifications_raw_results description: GET classifications raw_results source_operation: openapi/one-codex-openapi-original.json#get_classifications_raw_results - name: get_classifications_readlevel description: GET classifications readlevel source_operation: openapi/one-codex-openapi-original.json#get_classifications_readlevel - name: post_classifications_rerun description: POST classifications rerun source_operation: openapi/one-codex-openapi-original.json#post_classifications_rerun - name: get_classifications_results description: GET classifications results source_operation: openapi/one-codex-openapi-original.json#get_classifications_results - name: get_controls_instances description: GET controls instances source_operation: openapi/one-codex-openapi-original.json#get_controls_instances - name: get_controls_instances_public description: GET controls instances_public source_operation: openapi/one-codex-openapi-original.json#get_controls_instances_public - name: get_controls_self description: GET controls source_operation: openapi/one-codex-openapi-original.json#get_controls_self - name: post_controls_cancel description: POST controls cancel source_operation: openapi/one-codex-openapi-original.json#post_controls_cancel - name: get_controls_file_details description: GET controls file_details source_operation: openapi/one-codex-openapi-original.json#get_controls_file_details - name: delete_controls_files description: DELETE controls files source_operation: openapi/one-codex-openapi-original.json#delete_controls_files - name: get_controls_files description: GET controls files source_operation: openapi/one-codex-openapi-original.json#get_controls_files - name: get_controls_logs description: GET controls logs source_operation: openapi/one-codex-openapi-original.json#get_controls_logs - name: post_controls_rerun description: POST controls rerun source_operation: openapi/one-codex-openapi-original.json#post_controls_rerun - name: get_controls_results description: GET controls results source_operation: openapi/one-codex-openapi-original.json#get_controls_results - name: get_documents_instances description: GET documents instances source_operation: openapi/one-codex-openapi-original.json#get_documents_instances - name: post_documents_instances_confirm_upload description: POST documents instances_confirm_upload source_operation: openapi/one-codex-openapi-original.json#post_documents_instances_confirm_upload - name: post_documents_instances_init_multipart_upload description: Start a multipart upload directly to S3. source_operation: openapi/one-codex-openapi-original.json#post_documents_instances_init_multipart_upload - name: post_documents_instances_init_upload description: Deprecated in favour of init_multipart_upload source_operation: openapi/one-codex-openapi-original.json#post_documents_instances_init_upload - name: delete_documents_self description: DELETE documents source_operation: openapi/one-codex-openapi-original.json#delete_documents_self - name: get_documents_self description: GET documents source_operation: openapi/one-codex-openapi-original.json#get_documents_self - name: post_documents_add_user description: POST documents add_user source_operation: openapi/one-codex-openapi-original.json#post_documents_add_user - name: post_documents_download_uri description: POST documents download_uri source_operation: openapi/one-codex-openapi-original.json#post_documents_download_uri - name: post_documents_remove_user description: POST documents remove_user source_operation: openapi/one-codex-openapi-original.json#post_documents_remove_user - name: patch_documents_rename description: PATCH documents rename source_operation: openapi/one-codex-openapi-original.json#patch_documents_rename - name: get_events_instances description: GET events instances source_operation: openapi/one-codex-openapi-original.json#get_events_instances - name: get_events_self description: GET events source_operation: openapi/one-codex-openapi-original.json#get_events_self - name: get_functional_profiles_instances description: GET functional_profiles instances source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_instances - name: get_functional_profiles_instances_public description: GET functional_profiles instances_public source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_instances_public - name: get_functional_profiles_self description: GET functional_profiles source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_self - name: post_functional_profiles_cancel description: POST functional_profiles cancel source_operation: openapi/one-codex-openapi-original.json#post_functional_profiles_cancel - name: get_functional_profiles_file_details description: GET functional_profiles file_details source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_file_details - name: delete_functional_profiles_files description: DELETE functional_profiles files source_operation: openapi/one-codex-openapi-original.json#delete_functional_profiles_files - name: get_functional_profiles_files description: GET functional_profiles files source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_files - name: get_functional_profiles_filtered_results description: GET functional_profiles filtered_results source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_filtered_results - name: get_functional_profiles_logs description: GET functional_profiles logs source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_logs - name: post_functional_profiles_rerun description: POST functional_profiles rerun source_operation: openapi/one-codex-openapi-original.json#post_functional_profiles_rerun - name: get_functional_profiles_results description: GET functional_profiles results source_operation: openapi/one-codex-openapi-original.json#get_functional_profiles_results - name: get_genomes_instances description: GET genomes instances source_operation: openapi/one-codex-openapi-original.json#get_genomes_instances - name: get_genomes_self description: GET genomes source_operation: openapi/one-codex-openapi-original.json#get_genomes_self - name: get_jobs_instances description: GET jobs instances source_operation: openapi/one-codex-openapi-original.json#get_jobs_instances - name: post_jobs_instances description: POST jobs instances source_operation: openapi/one-codex-openapi-original.json#post_jobs_instances - name: get_jobs_self description: GET jobs source_operation: openapi/one-codex-openapi-original.json#get_jobs_self - name: patch_jobs_self description: PATCH jobs source_operation: openapi/one-codex-openapi-original.json#patch_jobs_self - name: get_jobs_details description: GET jobs details source_operation: openapi/one-codex-openapi-original.json#get_jobs_details - name: post_jobs_run description: POST jobs run source_operation: openapi/one-codex-openapi-original.json#post_jobs_run - name: get_metadata_instances description: GET metadata instances source_operation: openapi/one-codex-openapi-original.json#get_metadata_instances - name: get_metadata_self description: GET metadata source_operation: openapi/one-codex-openapi-original.json#get_metadata_self - name: patch_metadata_self description: PATCH metadata source_operation: openapi/one-codex-openapi-original.json#patch_metadata_self - name: get_mlsts_instances description: GET mlsts instances source_operation: openapi/one-codex-openapi-original.json#get_mlsts_instances - name: get_mlsts_instances_public description: GET mlsts instances_public source_operation: openapi/one-codex-openapi-original.json#get_mlsts_instances_public - name: get_mlsts_self description: GET mlsts source_operation: openapi/one-codex-openapi-original.json#get_mlsts_self - name: post_mlsts_cancel description: POST mlsts cancel source_operation: openapi/one-codex-openapi-original.json#post_mlsts_cancel - name: get_mlsts_file_details description: GET mlsts file_details source_operation: openapi/one-codex-openapi-original.json#get_mlsts_file_details - name: delete_mlsts_files description: DELETE mlsts files source_operation: openapi/one-codex-openapi-original.json#delete_mlsts_files - name: get_mlsts_files description: GET mlsts files source_operation: openapi/one-codex-openapi-original.json#get_mlsts_files - name: get_mlsts_logs description: GET mlsts logs source_operation: openapi/one-codex-openapi-original.json#get_mlsts_logs - name: post_mlsts_rerun description: POST mlsts rerun source_operation: openapi/one-codex-openapi-original.json#post_mlsts_rerun - name: get_mlsts_results description: GET mlsts results source_operation: openapi/one-codex-openapi-original.json#get_mlsts_results - name: get_panels_instances description: GET panels instances source_operation: openapi/one-codex-openapi-original.json#get_panels_instances - name: get_panels_instances_public description: GET panels instances_public source_operation: openapi/one-codex-openapi-original.json#get_panels_instances_public - name: get_panels_self description: GET panels source_operation: openapi/one-codex-openapi-original.json#get_panels_self - name: post_panels_cancel description: POST panels cancel source_operation: openapi/one-codex-openapi-original.json#post_panels_cancel - name: get_panels_file_details description: GET panels file_details source_operation: openapi/one-codex-openapi-original.json#get_panels_file_details - name: delete_panels_files description: DELETE panels files source_operation: openapi/one-codex-openapi-original.json#delete_panels_files - name: get_panels_files description: GET panels files source_operation: openapi/one-codex-openapi-original.json#get_panels_files - name: get_panels_logs description: GET panels logs source_operation: openapi/one-codex-openapi-original.json#get_panels_logs - name: post_panels_rerun description: POST panels rerun source_operation: openapi/one-codex-openapi-original.json#post_panels_rerun - name: get_panels_results description: GET panels results source_operation: openapi/one-codex-openapi-original.json#get_panels_results - name: get_projects_instances description: GET projects instances source_operation: openapi/one-codex-openapi-original.json#get_projects_instances - name: post_projects_instances description: POST projects instances source_operation: openapi/one-codex-openapi-original.json#post_projects_instances - name: get_projects_instances_public description: GET projects instances_public source_operation: openapi/one-codex-openapi-original.json#get_projects_instances_public - name: delete_projects_self description: DELETE projects source_operation: openapi/one-codex-openapi-original.json#delete_projects_self - name: get_projects_self description: GET projects source_operation: openapi/one-codex-openapi-original.json#get_projects_self - name: patch_projects_self description: PATCH projects source_operation: openapi/one-codex-openapi-original.json#patch_projects_self - name: post_projects_add_user description: POST projects add_user source_operation: openapi/one-codex-openapi-original.json#post_projects_add_user - name: post_projects_change_sharing description: POST projects change_sharing source_operation: openapi/one-codex-openapi-original.json#post_projects_change_sharing - name: get_projects_members description: GET projects members source_operation: openapi/one-codex-openapi-original.json#get_projects_members - name: post_projects_remove_user description: POST projects remove_user source_operation: openapi/one-codex-openapi-original.json#post_projects_remove_user - name: get_reports_instances description: GET reports instances source_operation: openapi/one-codex-openapi-original.json#get_reports_instances - name: get_reports_instances_public description: GET reports instances_public source_operation: openapi/one-codex-openapi-original.json#get_reports_instances_public - name: get_reports_self description: GET reports source_operation: openapi/one-codex-openapi-original.json#get_reports_self - name: post_reports_cancel description: POST reports cancel source_operation: openapi/one-codex-openapi-original.json#post_reports_cancel - name: get_reports_file_details description: GET reports file_details source_operation: openapi/one-codex-openapi-original.json#get_reports_file_details - name: delete_reports_files description: DELETE reports files source_operation: openapi/one-codex-openapi-original.json#delete_reports_files - name: get_reports_files description: GET reports files source_operation: openapi/one-codex-openapi-original.json#get_reports_files - name: get_reports_logs description: GET reports logs source_operation: openapi/one-codex-openapi-original.json#get_reports_logs - name: post_reports_rerun description: POST reports rerun source_operation: openapi/one-codex-openapi-original.json#post_reports_rerun - name: get_reports_results description: GET reports results source_operation: openapi/one-codex-openapi-original.json#get_reports_results - name: get_samples_instances description: GET samples instances source_operation: openapi/one-codex-openapi-original.json#get_samples_instances - name: post_samples_instances_cancel_upload description: POST samples instances_cancel_upload source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_cancel_upload - name: post_samples_instances_confirm_upload description: POST samples instances_confirm_upload source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_confirm_upload - name: post_samples_instances_import description: POST samples instances_import source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_import - name: post_samples_instances_init_multipart_upload description: Start a multipart upload directly to S3. source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_init_multipart_upload - name: post_samples_instances_init_upload description: POST samples instances_init_upload source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_init_upload - name: get_samples_instances_organization description: GET samples instances_organization source_operation: openapi/one-codex-openapi-original.json#get_samples_instances_organization - name: post_samples_instances_preupload description: POST samples instances_preupload source_operation: openapi/one-codex-openapi-original.json#post_samples_instances_preupload - name: get_samples_instances_public description: GET samples instances_public source_operation: openapi/one-codex-openapi-original.json#get_samples_instances_public - name: delete_samples_self description: DELETE samples source_operation: openapi/one-codex-openapi-original.json#delete_samples_self - name: get_samples_self description: GET samples source_operation: openapi/one-codex-openapi-original.json#get_samples_self - name: patch_samples_self description: PATCH samples source_operation: openapi/one-codex-openapi-original.json#patch_samples_self - name: post_samples_download_uri description: POST samples download_uri source_operation: openapi/one-codex-openapi-original.json#post_samples_download_uri - name: get_sequencing_instances_batches description: GET sequencing instances_batches source_operation: openapi/one-codex-openapi-original.json#get_sequencing_instances_batches - name: post_sequencing_instances_batches_register description: POST sequencing instances_batches_register source_operation: openapi/one-codex-openapi-original.json#post_sequencing_instances_batches_register - name: get_sequencing_batches description: GET sequencing batches source_operation: openapi/one-codex-openapi-original.json#get_sequencing_batches - name: get_sequencing_batches_samples description: GET sequencing batches_samples source_operation: openapi/one-codex-openapi-original.json#get_sequencing_batches_samples - name: get_tags_instances description: GET tags instances source_operation: openapi/one-codex-openapi-original.json#get_tags_instances - name: post_tags_instances description: POST tags instances source_operation: openapi/one-codex-openapi-original.json#post_tags_instances - name: get_tags_self description: GET tags source_operation: openapi/one-codex-openapi-original.json#get_tags_self - name: get_taxa_instances description: GET taxa instances source_operation: openapi/one-codex-openapi-original.json#get_taxa_instances - name: get_taxa_self description: GET taxa source_operation: openapi/one-codex-openapi-original.json#get_taxa_self - name: get_taxa_genomes description: GET taxa genomes source_operation: openapi/one-codex-openapi-original.json#get_taxa_genomes - name: get_taxa_parents description: GET taxa parents source_operation: openapi/one-codex-openapi-original.json#get_taxa_parents - name: get_taxa_reference_assembly description: GET taxa reference_assembly source_operation: openapi/one-codex-openapi-original.json#get_taxa_reference_assembly - name: get_users_instances description: GET users instances source_operation: openapi/one-codex-openapi-original.json#get_users_instances - name: get_users_self description: GET users source_operation: openapi/one-codex-openapi-original.json#get_users_self - name: get_webhooks_instances description: GET webhooks instances source_operation: openapi/one-codex-openapi-original.json#get_webhooks_instances - name: get_webhooks_self description: GET webhooks source_operation: openapi/one-codex-openapi-original.json#get_webhooks_self - name: get_workflows_instances description: GET workflows instances source_operation: openapi/one-codex-openapi-original.json#get_workflows_instances - name: get_workflows_instances_public description: GET workflows instances_public source_operation: openapi/one-codex-openapi-original.json#get_workflows_instances_public - name: get_workflows_self description: GET workflows source_operation: openapi/one-codex-openapi-original.json#get_workflows_self - name: post_workflows_cancel description: POST workflows cancel source_operation: openapi/one-codex-openapi-original.json#post_workflows_cancel - name: get_workflows_file_details description: GET workflows file_details source_operation: openapi/one-codex-openapi-original.json#get_workflows_file_details - name: delete_workflows_files description: DELETE workflows files source_operation: openapi/one-codex-openapi-original.json#delete_workflows_files - name: get_workflows_files description: GET workflows files source_operation: openapi/one-codex-openapi-original.json#get_workflows_files - name: get_workflows_logs description: GET workflows logs source_operation: openapi/one-codex-openapi-original.json#get_workflows_logs - name: post_workflows_rerun description: POST workflows rerun source_operation: openapi/one-codex-openapi-original.json#post_workflows_rerun - name: get_workflows_results description: GET workflows results source_operation: openapi/one-codex-openapi-original.json#get_workflows_results deployment: mode: none verified: derived tools: 170 checked: '2026-08-12' source: catalog MCP census